hzar.makeCline1DFreq: Make a cline model with the requested attributes.

In hzar: Hybrid Zone Analysis using R

Description

Constructs a clineMetaModel object for use with hzar.first.fitRequest.old.ML. Said object can be further tailored to the specific model desired, or can be used as-is.

Usage

hzar.makeCline1DFreq(data = NULL, scaling = "none", tails = "none",
  direction = NULL) 
hzar.makeCline1DCLT(data = NULL, scaling = "free", tails = "none",
  direction = NULL)
hzar.makeCline1DNormal(data, tails = "none")

Arguments

data	A hzar.obsData object, used to determine cline direction and estimate initial values.
scaling	Can be one of three strings: "none"A model with fixed minimum value 0 and maximum value 1 is desired. "fixed"A model with minimum and maximum values fixed to the minimum and maxumimum observed mean values of data is desired. "free"A model with the minimum and maximum value as free parameters is desired.
tails	Can be one of five strings: "none"A model with no exponential tails is desired "right"A model with just one exponential tail on the right is desired. "left"A model with just one exponential tail on the left is desired. "mirror"A model with two exponential tails mirrored about the cline center is desired. "both"A model with two tails with independent parameters is desired.
direction	Can be one of three values: NULLDetermine direction using data "ascending"A model whose estimates increase as the site distance increases is desired. "descending"A model whose estimates decrease as the site distance increases is desired.

Details

The clineMetaModel object returned by hzar.makeCline1DNormal has a slightly diffent structure, due to the complexity of the normal cline model. Use hzar.first.fitRequest.gC instead of hzar.first.fitRequest.old.ML to construct the hzar.fitRequest object needed for hzar.doFit.

Value

A clineMetaModel object, which is a list with the following 4 components:

req	A boolean function of the model parameters w
prior	Description of 'comp1'
func	Description of 'comp1'
parameterTypes	A list of clineParameter objects, named with the parameter names. A clineParameter object structure: Components: valThe initial or fixed value. wThe parameter tuning. Attributes: "param"The parameter name. "fixed"TRUE if the parameter is fixed. "limit.lower"The parameter minimum finite value. "limit.upper"The parameter maximum finite value. "realBTWN01"The parameter is restricted to between 0 and 1.

Author(s)

Graham Derryberry [e-mail]

References

Gay, L., P.-A. Crochet, D. A. Bell, and T. Lenormand. 2008. Comparing clines on molecular and phenotypic traits in hybrid zones: a window on tension zone models. Evolution 62:2789-2806.

Szymura, J., and N. H. Barton. 1986. Genetic analysis of a hybrid zone between the fire-bellied toads, Bombina bombina and B. variegata, near Cracow in souhern Poland. Evolution 40:1141-1159.

Szymura, J., and N. H. Barton. 1991. The genetic structure of the hybrid zone between the fire-bellied toads Bombina bombina and B. variegata: comparisons between transects and between loci. Evolution 45:237-261.

See Also

hzar.obsData hzar.first.fitRequest.old.ML hzar.first.fitRequest.gC

Examples

data(manakinMolecular);
mknAdaA <-
  hzar.doMolecularData1DPops(manakinMolecular$distance,
                             manakinMolecular$ada.A,
                             manakinMolecular$ada.nSamples);
mknAdaAmodel <-
  hzar.makeCline1DFreq(mknAdaA, scaling="fixed",tails="none");
str(mknAdaAmodel);

Example output

sh: 1: cannot create /dev/null: Permission denied
Loading required package: MCMCpack
Loading required package: coda
Loading required package: MASS
##
## Markov Chain Monte Carlo Package (MCMCpack)
## Copyright (C) 2003-2020 Andrew D. Martin, Kevin M. Quinn, and Jong Hee Park
##
## Support provided by the U.S. National Science Foundation
## (Grants SES-0350646 and SES-0350613)
##
Loading required package: foreach
List of 5
 $ prior         :function (center, width, pMin, pMax)  
 $ pExp          : language pMin + (pMax - pMin) * (1/(1 + exp(-((x - center) * 4/width))))
 $ req           :function (center, width, pMin, pMax)  
 $ parameterTypes:List of 4
  ..$ center:List of 2
  .. ..$ val: num 198
  .. ..$ w  : num 1.5
  .. ..- attr(*, "class")= chr "clineParameter"
  .. ..- attr(*, "param")= chr "center"
  .. ..- attr(*, "fixed")= logi FALSE
  .. ..- attr(*, "limit.lower")= num 0
  .. ..- attr(*, "limit.upper")= num 570
  .. ..- attr(*, "realBTWN01")= logi FALSE
  ..$ width :List of 2
  .. ..$ val: num 64.8
  .. ..$ w  : num 1.5
  .. ..- attr(*, "class")= chr "clineParameter"
  .. ..- attr(*, "param")= chr "width"
  .. ..- attr(*, "fixed")= logi FALSE
  .. ..- attr(*, "limit.lower")= num 0
  .. ..- attr(*, "limit.upper")= num 570
  .. ..- attr(*, "realBTWN01")= logi FALSE
  ..$ pMin  :List of 2
  .. ..$ val: num 0.1
  .. ..$ w  : num 1.1
  .. ..- attr(*, "class")= chr "clineParameter"
  .. ..- attr(*, "param")= chr "pMin"
  .. ..- attr(*, "fixed")= logi TRUE
  .. ..- attr(*, "limit.lower")= num 0
  .. ..- attr(*, "limit.upper")= num 1
  .. ..- attr(*, "realBTWN01")= logi TRUE
  ..$ pMax  :List of 2
  .. ..$ val: num 0.675
  .. ..$ w  : num 1.1
  .. ..- attr(*, "class")= chr "clineParameter"
  .. ..- attr(*, "param")= chr "pMax"
  .. ..- attr(*, "fixed")= logi TRUE
  .. ..- attr(*, "limit.lower")= num 0
  .. ..- attr(*, "limit.upper")= num 1
  .. ..- attr(*, "realBTWN01")= logi TRUE
 $ func          :function (center, width, pMin, pMax)  
 - attr(*, "class")= chr "clineMetaModel"
 - attr(*, "tails")= chr "none"

hzar documentation built on May 2, 2019, 7 a.m.